PLUMED-TUTORIALS

This lesson gives a introduction to the transition-tempered metadynamics (TTMetaD). The lesson is divided into two parts. The first part is a brief introduction to the TTMetaD method, and the second part is an exercise where you will apply the TTMetaD method to a simple system and a more advanced system - the dihedral angles of alanine dipeptide using vanilla MD TTMetaD and the GTP hydrolysis of the β-tubulin of a tubulin interdimer complex in microtubules using QM/MM TTMetaD, respectively.

The flow chart below shows the relationship between the different resources available for this lesson. The resources are divided into three categories: papers, tutorials, and instructions. The papers are the TTMetaD paper and the mechanism of MT-GTP hydrolysis paper. The tutorial is the basic MetaD tutorial. The flow chart shows that the TTMetaD paper is a prerequisite for the exercise, the MT-GTP paper is recommended but not required, and the MetaD tutorial is a previous tutorial that introduces the basics of MetaD. You can find the plumed input files of the two examples: the alanine dipeptide example and the GTP hydrolysis in microtubules example. You may click on the different boxes to access them.

flowchart TB;
    A[TTMetaD Paper] -.-> D[Instructions];
    B[MT-GTP Paper] -.-> D[Instructions];
    C[MetaD Tutorial] -.-> D[Instructions];
    D[Instructions] -.-> E[Alanine Dipeptide Example];
    D[Instructions] -.-> F[GTP Hydrolysis Example];
    click A "https://pubs.acs.org/doi/full/10.1021/ct500441q" "You should read this paper before completing this exercise"
    click B "https://www.pnas.org/doi/10.1073/pnas.2305899120" "You are recommended to read this paper but not required"
    click C "../../../21/004/data/NAVIGATION.html" "A previous tutorial that introduces the basics of MetaD"
    click D "INSTRUCTIONS.html" "Instructions for the exercise that you are supposed to complete"
    click E "alad/visualize.html" "Jupyter Notebook for the Alanine Dipeptide example"
    click F "mt_gtp/visualize.html" "Jupyter Notebook for the GTP hydrolysis in microtubules example"

Click here to open manual pages for actions discussed in this tutorial.